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GeneBe

1-165428805-G-C

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_006917.5(RXRG):c.211C>G(p.Arg71Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 33)

Consequence

RXRG
NM_006917.5 missense

Scores

1
5
13

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.106
Variant links:
Genes affected
RXRG (HGNC:10479): (retinoid X receptor gamma) This gene encodes a member of the retinoid X receptor (RXR) family of nuclear receptors which are involved in mediating the antiproliferative effects of retinoic acid (RA). This receptor forms dimers with the retinoic acid, thyroid hormone, and vitamin D receptors, increasing both DNA binding and transcriptional function on their respective response elements. This gene is expressed at significantly lower levels in non-small cell lung cancer cells. Alternatively spliced transcript variants have been described. [provided by RefSeq, Jun 2010]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
RXRGNM_006917.5 linkuse as main transcriptc.211C>G p.Arg71Gly missense_variant 2/10 ENST00000359842.10
RXRGNM_001256570.2 linkuse as main transcriptc.-217C>G 5_prime_UTR_variant 2/11

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RXRGENST00000359842.10 linkuse as main transcriptc.211C>G p.Arg71Gly missense_variant 2/101 NM_006917.5 P1
RXRGENST00000619224.1 linkuse as main transcriptc.-217C>G 5_prime_UTR_variant 2/111

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
33

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsJan 26, 2023The c.211C>G (p.R71G) alteration is located in exon 2 (coding exon 2) of the RXRG gene. This alteration results from a C to G substitution at nucleotide position 211, causing the arginine (R) at amino acid position 71 to be replaced by a glycine (G). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.11
BayesDel_addAF
Uncertain
0.052
T
BayesDel_noAF
Benign
-0.16
Cadd
Benign
18
Dann
Uncertain
0.98
DEOGEN2
Benign
0.41
T
Eigen
Benign
-0.60
Eigen_PC
Benign
-0.68
FATHMM_MKL
Benign
0.33
N
LIST_S2
Uncertain
0.93
D
M_CAP
Benign
0.080
D
MetaRNN
Uncertain
0.45
T
MetaSVM
Benign
-0.38
T
MutationAssessor
Benign
1.2
L
MutationTaster
Benign
0.68
N
PrimateAI
Pathogenic
0.81
D
PROVEAN
Benign
-0.080
N
REVEL
Uncertain
0.46
Sift
Benign
0.26
T
Sift4G
Benign
0.41
T
Polyphen
0.48
P
Vest4
0.73
MutPred
0.33
Gain of catalytic residue at V72 (P = 0.0211);
MVP
0.63
MPC
0.39
ClinPred
0.58
D
GERP RS
-2.9
Varity_R
0.11
gMVP
0.44

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr1-165398042; COSMIC: COSV100717262; COSMIC: COSV100717262; API